Docking pose detail

py3Dmol interaction viewer

Left: interactive complex viewer. Right: clickable PLIP-like interaction summary. Clicking an interaction thickens and highlights it in the 3D view.

Strict H-bonds Permissive H-bonds

Molecular report

Full metrics ↗

Reject Multiple quality flags — this pose should be deprioritised or discarded.

✓ Excellent LE (-1.395 kcal/mol/HA) ✓ Good fit quality (FQ -12.50) ✓ Strong H-bond network (11 bonds) ✗ Very high strain energy (25.5 kcal/mol) ✗ Geometry warnings ✗ Protein contact clashes ℹ SASA not computed

Score

-33.475

kcal/mol

-1.395

kcal/mol/HA

Fit Quality

-12.50

FQ (Leeson)

HAC

heavy atoms

369

LogP

1.63

cLogP

Strain ΔE

25.5 kcal/mol

SASA buried

computing…

Interaction summary

Collapsible panels

H-bonds 11 Hydrophobic 13 π–π 1 Clashes 4 Severe clashes 0 ⚠ Hydrophobic exposure 42%

⚠️Partial hydrophobic solvent exposure

43% of hydrophobic surface appears solvent-exposed (6/14 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

Non-polar atoms 14 Buried (contacted) 8 Exposed 6 LogP 1.63 H-bonds 11

Exposed fragments: phenyl (6/6 atoms exposed)

Final rank	2.988608026962566	Score	-33.4752
Inter norm	-1.29735	Intra norm	-0.0974499
Top1000	no	Excluded	no
Contacts	14	H-bonds	11
Artifact reason	geometry warning; 7 clashes; 4 protein contact clashes; high strain Δ 31.0
Residues	A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:MET163;A:NAP301;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174;A:VAL206

Protein summary

258 residues

Protein target	T08	Atoms	3881
Residues	258	Chains	2
Residue summary	LEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

Native ligand reference

★ reference

Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.

Name	TbPTR1_cW_6RX6_Ready	Contacts	19
Pose	Open native pose	H-bonds	6
IFP residues	A:ARG14; A:ASP161; A:CYS168; A:GLY205; A:LEU208; A:LEU209; A:LYS178; A:MET213; A:NAP301; A:PHE171; A:PHE97; A:PRO210; A:PRO99; A:SER207; A:SER95; A:TRP221; A:TYR174; A:TYR98; A:VAL206
Current overlap	13	Native recall	0.68
Jaccard	0.65	RMSD	-
H-bond strict	3	Strict recall	0.50
H-bond same residue+role	2	Role recall	0.40
H-bond same residue	3	Residue recall	0.60

Hydrogen bonds

Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

π–π interactions

Native π–π recall is disabled because no explicit native π–π reference was stored.

Hydrophobic contacts

Clashes

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	Contacts	Native overlap	Native recall	HB role recall	RMSD	Excluded
949	2.988608026962566	-1.29735	-33.4752	11	14	13	0.68	0.40	-	no	Current
1223	3.90227356618961	-0.951455	-23.0331	7	19	0	0.00	0.00	-	no	Open
1222	5.16710751599625	-0.883247	-18.9985	10	12	0	0.00	0.00	-	no	Open
950	8.673471239362351	-1.10259	-19.3974	11	14	12	0.63	0.40	-	yes	Open
1221	11.06728145974455	-1.32557	-38.5235	13	16	0	0.00	0.00	-	yes	Open
1224	11.7659767333244	-1.12609	-28.24	13	15	0	0.00	0.00	-	yes	Open

Molecular metrics

FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

✓ Metrics available

Scoring & efficiency

Docking score -33.475kcal/mol

Ligand efficiency (LE) -1.3948kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -12.500

LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe

Heavy atom count 24HA

Physicochemical properties

Molecular weight 369.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 1.63

Lipinski: ≤ 5

Rotatable bonds 7

Conformational strain (MMFF94s)

Strain energy (ΔE) 25.47kcal/mol

< 5 good · 5–10 marginal · > 10 problematic

Docked FF energy -16.43kcal/mol

Minimised FF energy -41.91kcal/mol

SASA & burial (FreeSASA)

not yet run

SASA has not been computed yet for this pose. It will be calculated automatically the next time this pose is loaded if a receptor PDB path is stored.

NMT-TY0931